Problems optimising a heme (Fe2+) group

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Sara Llap

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Sep 13, 2022, 10:00:25 AMSep 13
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Dear all, 

I am having problems on a geometry optimisation of a heme group with Fe2+ using PBE in CP2K. My calculations run and the total energy is decreasing. However, the job has been running for almost a month and it doesn't seem to converge. 

I am not an expert on CP2K nor on transition metals. I would really appreciate it if you could help me sort this out. I have  attached the restart file and the output for clarity. 

Thanks a lot, 


Sara
go.pbe.ini.rst10.out
HemHis_ini-1.restart

Ivan Gladich

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Sep 14, 2022, 1:06:23 AMSep 14
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Dear Sara

Not an expert of Heme but I think one problem could be the multiplicity (and charge?) of your system
Fe2+ in an aqueous solution should be high spin (Multiplicity 5)
In your input

    BASIS_SET_FILE_NAME BASIS_MOLOPT
     POTENTIAL_FILE_NAME GTH_POTENTIALS
     MULTIPLICITY  1
     CHARGE  -2


Check also for HEME


Hope it helps

Best
Ivan

Victor Volkov

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Sep 14, 2022, 3:24:48 AMSep 14
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Good morning Sara.
Several months ago there was a paper devoted to
electronic and structural properties of different hemes
to explain the color of blood
“Mapping blood biochemistry by Raman Spectroscopy at the cellular level.” Chem. Sci. 2022, 13, 133.
This may be relevant.
Victor


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Marcella Iannuzzi

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Sep 15, 2022, 11:57:21 AMSep 15
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Dear Sara

Before starting a geometry optimisation it is  good practice to get a converged single point calculation. 
If I understand correctly from the output you posted, this was not the case. 

I played a bit with the settings for your system and I got a converged single point calculation at the PBE level of theory 
for the molecule charged --2 (see the attached file).

Kind regards
Marcella
HemHis_ini_pbe_tz_bs_diag2_m2.inp

Sara Llap

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Sep 21, 2022, 5:30:55 PMSep 21
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Dear Ivan, Victor and Marcella, 

Thank you so much for your help. 

I have been reading the bibliography you suggested and using your inputs and I almost optimised the heme group. I got to a point where the optimisation does not seem to converge but it is really close. 

--------  Informations at step =   114 ------------

  Optimization Method        =                   SD

  Total Energy               =      -517.5364879764

  Real energy change         =         0.0000000050

  Decrease in energy         =                   NO

  Used time                  =              460.425


  Convergence check :

  Max. step size             =         0.0000000000

  Conv. limit for step size  =         0.0010000000

  Convergence in step size   =                  YES

  RMS step size              =         0.0000000000

  Conv. limit for RMS step   =         0.0010000000

  Convergence in RMS step    =                  YES

  Max. gradient              =         0.0012644252

  Conv. limit for gradients  =         0.0010000000

  Conv. for gradients        =                   NO

  RMS gradient               =         0.0002927175

  Conv. limit for RMS grad.  =         0.0010000000

  Conv. in RMS gradients     =                  YES

 ---------------------------------------------------


I have been playing a bit with the parameters but I haven't managed to make it work. 


Thanks again, 

Kind regards, 


Sara


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HemHis_ini_pbe_tz_bs_diag2_m2-1.restart
marcella.ini.go3.out

Marcella Iannuzzi

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Sep 22, 2022, 3:39:20 AMSep 22
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Dear Sara 

Starting around step 50 the coordinates do not change anymore
Max. step size             =         0.0000000000
The gradient  above tolerance is only one. It is the x component of the force on atom 47, a hydrogen. 
It remains practically constant for many steps.
It seems that the optimisation algorithm is not in the conditions of performing any CG step, and the SD gets stuck. 
So since step 50 nothing changes in the structure.
I would try and change the optimiser to BFGS.

Kind regards
Marcella

Sara Llap

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Nov 13, 2022, 5:52:53 PMNov 13
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Dear Marcella, 

Thank you for your help. It took me a lot of attempts but I managed to converge the calculation. 

Thank you again!

Sara

Sara Llap

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Dec 2, 2022, 12:04:40 PM (yesterday) Dec 2
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Dear Marcella, 

I used your advice on several other calculations and it worked but I struggle with one that I am unable to converge the SCF. Could you help me or give some advice on how to solve this issue?

The initial structure comes from a PM6 calculation. 

Thank you very much in advance, 

Sara
end.pbe.out
end.pbe.inp
HemHis_end.xyz
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